Hongkai’s Research Group

Book Chapters, Thesis and Others

(* corresponding author, § equal contribution, bold: lab members and advisees)


Other Articles and Editorials (Not Peer Reviewed)

1. Rudin C, Dunson D, Irizarry R, Ji HK, Laber E, Leek J, McCormick T, Rose S, Schafer C, van der Laan M, Wasserman L, Xue L. (2014) Discovery with data: Leveraging statistics with computer science to transform science and society. American Statistical Association White Paper


Book Chapters

2. Ji ZC, Ji HK (2019) Pseudotime Reconstruction Using TSCAN. Computational Methods for Single-Cell Data Analysis, pp 115-124, Edited by Guo-Cheng Yuan, Humana Press, Springer

3. Wei YY, Tenzen T and Ji HK (2016) Cormotif: An R package for jointly detecting differential gene expression in multiple studies. Computational Biology and Bioinformatics, pp 28-47. Edited by Ka-Chun Wong, CRC Press

4. Ji HK* and Wei YY (2015) Integrative Analysis of Multiple ChIP-X Data Sets Using  Correlation Motifs. Integrating Omics Data, edited by George C. Tseng, Debashis Ghosh, Xianghong Jasmine Zhou, pp 110-133. Cambridge University Press [Link]

5. Wu H and Ji HK* (2012) JAMIE: A Software Tool for Jointly Analyzing Multiple ChIP-chip Experiments. Methods Mol Biol. (Next Generation Microarray Bioinformatics edited by Junbai Wang, Aik C Tang, Tianhai Tian)  802: 363-375 [Link]

6. Ji HK, Jiang H, Ma WX and Wong WH (2011) Using CisGenome to Analyze ChIP-chip and ChIP-seq Data. Current Protocols in Bioinformatics, 2011 Mar, Chapter 2: Unit2.13. Wiley. [Link]

7. Ji HK (2011) Computational Analysis of ChIP-chip Data. In the Handbook of Computational Statistics, Part 2, 257-282, DOI: 10.1007/978-3-642-16345-6_12 (edited by Henry Horng-Shing Lu, Bernhard Schölkopf and Hongyu Zhao) [Link]

8. Ji HK (2010) Computational Analysis of ChIP-seq Data. Methods Mol Biol. (Computational Biology of Transcription Factor Binding edited by Istvan Ladunga) 674: 143-159 [Link]

9. Cullen P et al. including Ji HK (2004) Computational methods and bioinformatic tools. In Analysing Gene Expression, edited by Lorkowski S and Cullen P, pp 769-904, Wiley-VCH Verlag GmbH & Co. KGaA



10. Ji HK (PhD Thesis): Towards Deciphering Gene Regulatory Networks in Mammalian Genomes: Statistical Models and a Case Study. Harvard University, 2007

11. Ji HK (Master’s Thesis): Analysis of Alternative Splicing and Complex Disease based on Population Comparisons. Tsinghua University, 2002


Technical Reports

12. Ji HK and Wong WH. (2005) Increasing power of microarray gene selection: an empirical Bayes approach (Harvard Qualifying Paper) [Link] [Supplementary Notes] [Supporting Website: PowerExpress]